First off ...
Now do you have anything done to the bike? Like added neon's or something like that? Removed lights and or added anything like this?
Are you doing anything special while the bike cuts out? How often has this problem happened? Same day different days?
I am not a expert here but since Honda said everything was fine and the computer has not error codes in it. Then it should be good.
But I would try and get my hands on another ECU and try that out and see if it helps. Also you might want to check the guages. I know when you unplug them you will reset the clock and the bike will not run with out them ..